Using a new exoIII footprinting assay, we have purified Drosophila heat shock gene activator protein to homogeneity. The protein migrates with a mass of 110 kilo daltons on denaturing gels; its binding activity is detectable within minutes of heat shock. The binding occurs with high affinity (KD = 4 x 10-12M) to the heat shock control sequence. The exoIII footprinting technique has been applied successfully to the Drosophila heat shock gene TATA box sequence, and to the rat insulin II gene and the Drosophila segmentation gene fushi tarazu.